library(openxlsx)
# allC = merge(p1C,p2C,by.x="Sample",by.y="Sample")
popsOfInterestFile="/Volumes/Beta/data/flow/results_r25_25full_SS_SubCD8_SCD14_Manuals/finalCounts/popsOfInterest.txt"
popsOfInterest=read.delim(popsOfInterestFile, stringsAsFactors = FALSE, sep = "\t")
popsOfInterest$POPCOMP=gsub(" ",".",popsOfInterest$POPCOMP)
popsOfInterest$POPF=gsub(" ",".",popsOfInterest$POPF)
popsOfInterest$POPHRS1000=gsub(" ",".",popsOfInterest$POPHRS1000)
popsOfInterest$POPM=gsub(" ",".",popsOfInterest$POPM)
# popsOfInterest$POPM=gsub(")",".",popsOfInterest$POPM,fixed = TRUE)
# popsOfInterest$POPM=gsub("(",".",popsOfInterest$POPM,fixed = TRUE)
popsOfInterest$POPJ=gsub(" ",".",popsOfInterest$POPJ)
popsOfInterest$POPJ=gsub(")",".",popsOfInterest$POPJ,fixed = TRUE)
popsOfInterest$POPJ=gsub("(",".",popsOfInterest$POPJ,fixed = TRUE)
releasedFile="/Volumes/Beta/data/flow/results_r25_25full_SS_SubCD8_SCD14_Manuals/FULL/releasedSamples.txt"
released = read.delim(releasedFile,
header = TRUE,
stringsAsFactors = FALSE)
noBadsFile="/Users/Kitty/git/auto-fcs/explore/openCyto/extractManualComp/manualUse.txt"
noBads = read.delim(noBadsFile,
header = TRUE,
stringsAsFactors = FALSE)
dir="/Volumes/Beta/data/flow/results_r25_25full_SS_SubCD8_SCD14_Manuals/finalCountsFreqCBC/"
p1="p1.cnts.frqs.cbcs.xlsx"
p2="p2.all-01-23-17.xlsx"
p2Test=read.xlsx(paste0(dir,"p2.all-01-23-17.xlsx"), sheet=1,check.names = TRUE)
for(thing in colnames(p2Test)){
print(paste0(thing, " ",max(as.numeric(p2Test[,c(thing)]),na.rm = TRUE) ))
}
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## Warning in max(as.numeric(p2Test[, c(thing)]), na.rm = TRUE): no non-
## missing arguments to max; returning -Inf
## [1] "Sample -Inf"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): no non-missing arguments to max; returning -Inf
## [1] "MACHINE -Inf"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): no non-missing arguments to max; returning -Inf
## [1] "F_ID -Inf"
## [1] "DATE 43024"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): no non-missing arguments to max; returning -Inf
## [1] "EXPERIMENTER -Inf"
## [1] "SourceCode.0.Std.1.Manual.2.DCSub.3.OCFail 3"
## [1] "Dupl 1"
## [1] "MonoRecompute 1"
## Warning in max(as.numeric(p2Test[, c(thing)]), na.rm = TRUE): no non-
## missing arguments to max; returning -Inf
## [1] "COUNTS. -Inf"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## [1] "Live.Single.PBMCs 1090134"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## [1] "DC.NK.MONOCYTES 338328"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## [1] "DC.NK 323681"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## [1] "DC 86443"
## [1] "NK 299108"
## [1] "MONOCYTES 209922"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## [1] "MonoRecomp 209922"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## [1] "Myeloid.DC 80490"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## [1] "Plasmacytoid.DC 46443"
## [1] "NK.CD56HI 8179"
## [1] "NK.CD56LO 295577"
## [1] "NK.CD56LO.Fixed 295068"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## [1] "Classical.monocytes 179752"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## [1] "Non.classical.monocytes 57859"
## Warning in max(as.numeric(p2Test[, c(thing)]), na.rm = TRUE): no non-
## missing arguments to max; returning -Inf
## [1] "FREQS. -Inf"
## [1] "DC.NK.MONOCYTES.1 0.970588235294118"
## [1] "DC.NK.1 0.846153846153846"
## [1] "DC.1 0.846153846153846"
## [1] "NK.1 0.487232957105566"
## [1] "MonoRecomp.1 0.870967741935484"
## [1] "Myeloid.DC.1 1"
## [1] "Plasmacytoid.DC.1 1"
## [1] "NK.CD56HI.1 0.419505404520144"
## [1] "NK.CD56LO.Fixed.1 1"
## [1] "Classical.monocytes.1 1"
## [1] "Non.classical.monocytes.1 0.950877596634236"
## Warning in max(as.numeric(p2Test[, c(thing)]), na.rm = TRUE): no non-
## missing arguments to max; returning -Inf
## [1] "CBCs -Inf"
## Warning in paste0(thing, " ", max(as.numeric(p2Test[, c(thing)]), na.rm =
## TRUE)): NAs introduced by coercion
## [1] "WBC 205.3"
## [1] "DC.NK.MONOCYTES.2 7.19753583698614"
## [1] "DC.NK.2 7.1424712711764"
## [1] "DC.2 6.84563440350669"
## [1] "NK.2 3.07757879605184"
## [1] "MonoRecomp.2 3.39677419354839"
## [1] "Myeloid.DC.2 2.07425660466769"
## [1] "Plasmacytoid.DC.2 4.40165857125933"
## [1] "NK.CD56HI.2 0.0777116529084277"
## [1] "NK.CD56LO.Fixed.2 2.59252958632518"
## [1] "Classical.monocytes.2 2.89354838709677"
## [1] "Non.classical.monocytes.2 0.804579925650557"
addCols=c("Sample", "Manual", "MACHINE", "F_ID", "DATE", "EXPERIMENTER")
sheets = list(c("COUNTS",1),c("FREQ",2),c("CBCS",3))
parse <- function(dir,p,sheet,extractPop,addCols,manualRms) {
pd= read.xlsx(paste0(dir,p), sheet=as.numeric(sheet[2]))
colnames(pd) =gsub("Manual.*","Manual",colnames(pd))
colnames(pd) =gsub(".Fixed","",colnames(pd),fixed = TRUE)
extract = c(addCols,extractPop[!is.na(extractPop)])
have=( extract %in% colnames(pd))
print(table(have))
print(extract[have])
pE = pd[,extract[have]]
pE$METRIC=sheet[1]
#
use = (pE$F_ID %in% manualRms$Study.ID)
pE$RELEASED=use
return(pE)
}
p1All=data.frame()
p2All=data.frame()
p1Filt = read.xlsx(paste0(dir,p1), sheet=1)
namesP1=p1Filt[which(p1Filt$`Live.cells.(PE-)`>20000),]$Sample
for(sheet in sheets){
p1d=parse(dir=dir,p=p1,sheet=sheet,extractPop =popsOfInterest$POPM,addCols = addCols,manualRms=released )
usep1=p1d$Sample %in% namesP1
p1d=p1d[usep1,]
p1All=rbind(p1All,p1d)
#
#
# p2d=parse(dir=dir,p=p2,sheet=sheet,extractPop =popsOfInterest$POPCOMP,addCols = addCols,manualRms=released )
# usep2=p2d$Sample %in% namesP2
# p2d=p2d[usep2,]
# #
# # usep2=p2d$Sample %in% noBads$x
# # p2d=p2d[usep2,]
#
# print(colnames(p2d))
# print(colnames(p2All))
#
# p2All=rbind(p2All,p2d)
}
## have
## FALSE TRUE
## 11 13
## [1] "Sample" "Manual"
## [3] "MACHINE" "F_ID"
## [5] "DATE" "EXPERIMENTER"
## [7] "naive.Bcells.(CD27-.IgD+)" "cytotoxic.Tcells-CD8+"
## [9] "Tcells.(CD3+.CD19-)" "IgD-.memory.Bcells.(CD27+)"
## [11] "IgD+.memory.Bcells.(CD27+)" "Helper.Tcells-CD4+"
## [13] "B.cells.(CD3-.CD19+)"
## have
## FALSE TRUE
## 11 13
## [1] "Sample" "Manual"
## [3] "MACHINE" "F_ID"
## [5] "DATE" "EXPERIMENTER"
## [7] "naive.Bcells.(CD27-.IgD+)" "cytotoxic.Tcells-CD8+"
## [9] "Tcells.(CD3+.CD19-)" "IgD-.memory.Bcells.(CD27+)"
## [11] "IgD+.memory.Bcells.(CD27+)" "Helper.Tcells-CD4+"
## [13] "B.cells.(CD3-.CD19+)"
## have
## FALSE TRUE
## 11 13
## [1] "Sample" "Manual"
## [3] "MACHINE" "F_ID"
## [5] "DATE" "EXPERIMENTER"
## [7] "naive.Bcells.(CD27-.IgD+)" "cytotoxic.Tcells-CD8+"
## [9] "Tcells.(CD3+.CD19-)" "IgD-.memory.Bcells.(CD27+)"
## [11] "IgD+.memory.Bcells.(CD27+)" "Helper.Tcells-CD4+"
## [13] "B.cells.(CD3-.CD19+)"
p1All$DATE=as.Date(p1All$DATE,origin='1899-12-30')
## Warning in strptime(xx, f <- "%Y-%m-%d", tz = "GMT"): unknown timezone
## 'zone/tz/2017c.1.0/zoneinfo/America/Chicago'
p2All=read.xlsx(paste0(dir,"p2.all.xlsx"), sheet=1,check.names = TRUE)
p2All=p2All[which(p2All$Live.Single.PBMCs>20000),]
p2All$DATE=as.Date(p2All$DATE, origin = '1899-12-30')
p2All$Manual=p2All$SourceCode.0.Std.1.Manual.2.DCSub.3.OCFail
p2All$Manual=gsub("2","0",p2All$Manual)
# p2All$Manual=gsub("1","0",p2All$Manual)
colnames(p2All) =gsub(".Fixed","",colnames(p2All),fixed = TRUE)
p2All=p2All[which(p2All$Dupl==1),]
# table((as.numeric(p2All$Classical.monocytes))>as.numeric(p2All$MONOCYTES))
# p2All$Manual=gsub("3","0",p2All$Manual)
use = (p2All$F_ID %in% released$Study.ID)
p2All$RELEASED=use
releaseP2= p2All[use,]
# p2All[which(p2All$DC>60000&p2All$METRIC=="COUNTS"),]$F_ID
# p2All$DATE_MONTH <- as.Date(cut(as.Date(p2All$DATE),
# breaks = "month"))
# pAll$DATE_MONTH <- as.Date(cut(as.Date(pAll$DATE),
# breaks = "month"))
popsOfInterest$PANEL1= popsOfInterest$POPM %in% colnames(p1All)
popsOfInterest$PANEL2= popsOfInterest$POPCOMP %in% colnames(p2All)
p1JflowCounts= read.delim("/Volumes/Beta/data/flow/compManual/p1.cnts.xln", stringsAsFactors = FALSE)
p1JflowCounts$Sample=p1JflowCounts$FILE
p2JflowCounts= read.delim("/Volumes/Beta/data/flow/compManual/p2.cnts.xln", stringsAsFactors = FALSE)
p2JflowCounts$Sample=p2JflowCounts$FILE
origPercents =read.xlsx("/Volumes/Beta/data/flow/HRS1000 REPORT.xlsx", sheet=1)
origCBCs =read.xlsx("/Volumes/Beta/data/flow/HRS1000 REPORT.xlsx", sheet=3)
origPercentP2 =read.xlsx("/Volumes/Beta/data/flow/p2.newGateTree.xlsx", sheet=2)
origPercentP2$Sample=gsub(".*/","",origPercentP2$X1)
releaseP2$HAVE= (releaseP2$Sample %in% origPercentP2$Sample)
library(ggplot2)
t2 <- theme(
axis.line = element_line(colour = "black"),
axis.text = element_text(colour = "black"),
axis.ticks = element_line(colour = "black"),
# panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
# panel.grid.major.y = element_blank(),
panel.grid.minor.y = element_blank(),
panel.border = element_blank(),
panel.background = element_blank(),
# legend.position="none",
axis.text.x=element_text(angle=90,hjust=1)
)
theme_set(theme_grey(base_size = 18))
summarize <- function(oc,manual,mergeOCCol,mergeManCol,ocCol,manualCol) {
merge=merge(oc,manual,by.x=mergeOCCol,by.y=mergeManCol)
print(table(merge$Manual))
numManuals=length(merge[which(merge$Manual=="1"),][,ocCol])
merge=merge[which(merge$Manual=="0"&merge$RELEASED),]
t1 =cor.test(as.numeric(merge[,c(ocCol)]),as.numeric(merge[,c(manualCol)]),method = "pearson",na.action="na.omit")
t2=cor.test(as.numeric(merge[,c(ocCol)]),as.numeric(merge[,c(manualCol)]),method = "spearman",na.action="na.omit")
medianOCFreq=median(as.numeric(merge[,c(ocCol)]),na.rm = TRUE)
meanOCFreq=mean(as.numeric(merge[,c(ocCol)]),na.rm = TRUE)
sdOCFreq=sd(as.numeric(merge[,c(ocCol)]),na.rm = TRUE)
# print(plot(as.numeric(merge[,c(ocCol)]),as.numeric(merge[,c(manualCol)])))
medianManualFreq=median(as.numeric(merge[,c(manualCol)]),na.rm = TRUE)
meanManualFreq=mean(as.numeric(merge[,c(manualCol)]),na.rm = TRUE)
sdManualFreq=sd(as.numeric(merge[,c(manualCol)]),na.rm = TRUE)
g= ggplot(merge,aes(x=as.numeric(merge[,c(ocCol)]),y=as.numeric(merge[,c(manualCol)]))) +
geom_point() +
xlab(paste0("OC ",ocCol)) +
ylab(paste0("Manual ",ocCol))+ggtitle(paste0("pearson = ",t1$estimate, "\n spearman = ", t2$estimate, "\nn=", length(merge[,c(ocCol)]) ))
print(g)
tmp = data.frame(
OC_POP = ocCol,
ManualPop = manualCol,
N = length(merge[,c(ocCol)]),
PEARSON = t1$estimate,
SPEARMAN = t2$estimate,
MEDIAN_OC = medianOCFreq,
MEDIAN_MANUAL = medianManualFreq,
ABS_DIFF_MEDIAN = abs(medianOCFreq-medianManualFreq),
MEAN_OC = meanOCFreq,
MEAN_MANUAL = meanManualFreq,
ABS_DIFF_MEAN = abs(meanOCFreq-meanManualFreq),
SD_OC = sdOCFreq,
SD_MANUAL = sdManualFreq,
ABS_DIFF_SD = abs(sdOCFreq-sdManualFreq),
NUM_MANUALS_REMOVED=numManuals
)
return(tmp)
}
forMerge=c("Sample","DATE" , "MACHINE" , "EXPERIMENTER")
stats <- function(data,machine=TRUE) {
require(MASS)
formula <- TARGET ~ DATE + MACHINE + EXPERIMENTER
if(!machine){
formula <- TARGET ~ DATE + EXPERIMENTER
}
fit <- lm(formula, data = data)
step <- stepAIC(fit, direction = "both")
t=summary(step)
ps=as.data.frame(t$coefficients)
f=summary(eval(t$call))
result=paste0("MODEL=",t$call[2],";MODEL_ADJ_R_SQUARED=",f$adj.r.squared," ;pvals=",paste0(ps$`Pr(>|t|)`[2:length(ps$`Pr(>|t|)`)],collapse = ","))
return(result)
# print(step$anova)
}
results=data.frame()
for(pop in popsOfInterest$POPM){
if(!is.na(pop)){
for(metric in sheets){
jflow=popsOfInterest[which(popsOfInterest$POPM==pop),]$POPJ
origColumn=popsOfInterest[which(popsOfInterest$POPM==pop),]$POPHRS1000
compLook=popsOfInterest[which(popsOfInterest$POPM==pop),]$POPM
if(popsOfInterest[which(popsOfInterest$POPM==pop),]$PANEL1){
print(paste0(pop," panel1 ",metric[1]))
if(metric[1]=="COUNTS"){
tmp =summarize(p1All[which(p1All$METRIC==metric[1]),],p1JflowCounts,"Sample","Sample",pop,jflow)
tmp$METRIC=metric[1]
tmp$PANEL="panel1"
tmp$NUM_MANUAL_POPS_ZEROED_OUT=NA
tmp$COMP_LOOK=compLook
tmp$CONFOUNDING_MODEL_OC_ALL_SAMPLES=NA
tmp$CONFOUNDING_MODEL_OC_MANUAL_MATCHED=NA
tmp$CONFOUNDING_MODEL_MANUAL=NA
results=rbind(results,tmp)
} else if(metric[1]=="FREQ"){
useOrigPercents =origPercents[which(origPercents[,c(origColumn)]<1000),]
tmp =summarize(p1All[which(p1All$METRIC==metric[1]),],useOrigPercents,"F_ID","Study.ID",pop,origColumn)
tmp$METRIC=metric[1]
tmp$PANEL="panel1"
tmp$NUM_MANUAL_POPS_ZEROED_OUT=length(origPercents[,c(origColumn)])-length(useOrigPercents[,c(origColumn)])
tmp$COMP_LOOK=compLook
tmp$CONFOUNDING_MODEL_OC_ALL_SAMPLES=NA
tmp$CONFOUNDING_MODEL_OC_MANUAL_MATCHED=NA
tmp$CONFOUNDING_MODEL_MANUAL=NA
results=rbind(results,tmp)
}
}else if(popsOfInterest[which(popsOfInterest$POPM==pop),]$PANEL2){
print(paste0(pop," panel2 ",metric[1]))
if(metric[1]=="COUNTS"){
popCompOC =paste0(popsOfInterest[which(popsOfInterest$POPM==pop),]$POPCOMP)
tmp =summarize(p2All,p2JflowCounts,"Sample","Sample",popCompOC,jflow)
tmp$METRIC=metric[1]
tmp$PANEL="panel2"
tmp$NUM_MANUAL_POPS_ZEROED_OUT=NA
tmp$COMP_LOOK=compLook
subData=p2All
subData$TARGET=as.numeric(subData[,c(popCompOC)])
tmp$CONFOUNDING_MODEL_OC_ALL_SAMPLES=NA
r= stats(subData)
tmp$CONFOUNDING_MODEL_OC_ALL_SAMPLES=r
tmp$CONFOUNDING_MODEL_OC_MANUAL_MATCHED=NA
tmp$CONFOUNDING_MODEL_MANUAL=NA
results=rbind(results,tmp)
} else if(metric[1]=="FREQ"){
popCompOC =paste0(popsOfInterest[which(popsOfInterest$POPM==pop),]$POPCOMP,".1")
ocColumnTmp=popsOfInterest[which(popsOfInterest$POPM==pop),]$POPCOMP
useOrigPercents =origPercentP2[which(origPercentP2[,c(ocColumnTmp)]<1000),]
origTmp=ocColumnTmp
if(ocColumnTmp==origTmp){
# ocColumnTmp=paste0(ocColumnTmp,".x")
origTmp=paste0(origTmp,".y")
}
if(popCompOC=="MONOCYTES.1"){
popCompOC="MonoRecomp.1"
}
tmp =summarize(p2All,origPercentP2[,c("Sample",ocColumnTmp)],"Sample","Sample",popCompOC,origTmp)
oc=p2All
manual=origPercentP2
mergeOCCol="Sample"
mergeManCol="Sample"
ocCol=popCompOC
manualCol=origTmp
tmp$METRIC=metric[1]
tmp$PANEL="panel2"
tmp$NUM_MANUAL_POPS_ZEROED_OUT=length(origPercentP2[,c(popsOfInterest[which(popsOfInterest$POPM==pop),]$POPCOMP)])-length(useOrigPercents[,c(popsOfInterest[which(popsOfInterest$POPM==pop),]$POPCOMP)])
tmp$COMP_LOOK=compLook
tmp$CONFOUNDING_MODEL_OC_ALL_SAMPLES=NA
subDataP2=p2All[which(p2All$Manual=="0"),]
subDataP2$TARGET=as.numeric(subDataP2[,c(popCompOC)])
r= stats(subDataP2)
tmp$CONFOUNDING_MODEL_OC_ALL_SAMPLES=r
forMergeHere =c(forMerge,popCompOC)
subData=origPercentP2
subData =merge(subDataP2[,forMergeHere],subData,by.x = "Sample",by.y = "Sample")
subData$TARGET=as.numeric(subData[,popCompOC])
r= stats(subData,machine = FALSE)
tmp$CONFOUNDING_MODEL_OC_MANUAL_MATCHED=r
subData$TARGET=as.numeric(subData[,ocColumnTmp])
tmp$CONFOUNDING_MODEL_MANUAL =NA
r= stats(subData,machine = FALSE)
tmp$CONFOUNDING_MODEL_MANUAL=r
results=rbind(results,tmp)
}
}
}
}
}
## [1] "naive.Bcells.(CD27-.IgD+) panel1 COUNTS"
##
## 0 1
## 928 31
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "naive.Bcells.(CD27-.IgD+) panel1 FREQ"
##
## 0 1
## 924 33
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "naive.Bcells.(CD27-.IgD+) panel1 CBCS"
## [1] "cytotoxic.Tcells-CD8+ panel1 COUNTS"
##
## 0 1
## 928 31
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "cytotoxic.Tcells-CD8+ panel1 FREQ"
##
## 0 1
## 924 33
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "cytotoxic.Tcells-CD8+ panel1 CBCS"
## [1] "Tcells.(CD3+.CD19-) panel1 COUNTS"
##
## 0 1
## 928 31
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "Tcells.(CD3+.CD19-) panel1 FREQ"
##
## 0 1
## 924 33
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "Tcells.(CD3+.CD19-) panel1 CBCS"
## [1] "IgD-.memory.Bcells.(CD27+) panel1 COUNTS"
##
## 0 1
## 928 31
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "IgD-.memory.Bcells.(CD27+) panel1 FREQ"
##
## 0 1
## 853 19
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "IgD-.memory.Bcells.(CD27+) panel1 CBCS"
## [1] "IgD+.memory.Bcells.(CD27+) panel1 COUNTS"
##
## 0 1
## 928 31
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "IgD+.memory.Bcells.(CD27+) panel1 FREQ"
##
## 0 1
## 853 19
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "IgD+.memory.Bcells.(CD27+) panel1 CBCS"
## [1] "Helper.Tcells-CD4+ panel1 COUNTS"
##
## 0 1
## 928 31
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "Helper.Tcells-CD4+ panel1 FREQ"
##
## 0 1
## 924 33
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "Helper.Tcells-CD4+ panel1 CBCS"
## [1] "B.cells.(CD3-.CD19+) panel1 COUNTS"
##
## 0 1
## 928 31
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "B.cells.(CD3-.CD19+) panel1 FREQ"
##
## 0 1
## 924 33
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## [1] "B.cells.(CD3-.CD19+) panel1 CBCS"
## [1] "Non.classical.monocytes.(CD16+.CD14+) panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Warning: NAs introduced by coercion
## Loading required package: MASS
## Start: AIC=123745.8
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 2.7232e+10 123746
## - MACHINE 1 15175858 2.7247e+10 123748
## - DATE 1 36281500 2.7268e+10 123755
## - EXPERIMENTER 4 185602394 2.7417e+10 123794
## [1] "Non.classical.monocytes.(CD16+.CD14+) panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Start: AIC=-48307.56
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - MACHINE 1 0.000121 10.764 -48309
## <none> 10.764 -48308
## - DATE 1 0.031726 10.796 -48288
## - EXPERIMENTER 4 0.079288 10.844 -48261
##
## Step: AIC=-48309.48
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 10.764 -48309
## + MACHINE 1 0.000121 10.764 -48308
## - DATE 1 0.034991 10.800 -48287
## - EXPERIMENTER 4 0.082070 10.847 -48261
## Start: AIC=-3831.02
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 0.0023316 2.1347 -3832.3
## - EXPERIMENTER 2 0.0119431 2.1444 -3831.3
## <none> 2.1324 -3831.0
##
## Step: AIC=-3832.29
## TARGET ~ EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 2 0.0124809 2.1472 -3832.4
## <none> 2.1347 -3832.3
## + DATE 1 0.0023316 2.1324 -3831.0
##
## Step: AIC=-3832.39
## TARGET ~ 1
##
## Df Sum of Sq RSS AIC
## <none> 2.1472 -3832.4
## + EXPERIMENTER 2 0.0124809 2.1347 -3832.3
## + DATE 1 0.0028694 2.1444 -3831.3
## Start: AIC=-4515.96
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 0.76483 -4516.0
## - EXPERIMENTER 2 0.0076323 0.77246 -4513.3
## - DATE 1 0.0172399 0.78207 -4503.1
## [1] "Non.classical.monocytes.(CD16+.CD14+) panel2 CBCS"
## [1] "Myeloid.DC.(CD11c+.CD123-) panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Warning: NAs introduced by coercion
## Start: AIC=136526.6
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 1.2885e+11 136527
## - DATE 1 53534386 1.2891e+11 136528
## - MACHINE 1 121561868 1.2897e+11 136532
## - EXPERIMENTER 4 3108951365 1.3196e+11 136715
## [1] "Myeloid.DC.(CD11c+.CD123-) panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Start: AIC=-31093.11
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 110.25 -31093
## - MACHINE 1 0.35563 110.61 -31071
## - DATE 1 0.49103 110.74 -31062
## - EXPERIMENTER 4 0.73043 110.98 -31052
## Start: AIC=-2797.4
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 10.020 -2797.4
## - EXPERIMENTER 2 0.18831 10.208 -2789.0
## - DATE 1 0.24052 10.261 -2783.6
## Start: AIC=-2859.96
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 0.00289 9.1271 -2861.8
## <none> 9.1242 -2860.0
## - EXPERIMENTER 2 0.51703 9.6413 -2827.1
##
## Step: AIC=-2861.75
## TARGET ~ EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 9.1271 -2861.8
## + DATE 1 0.00289 9.1242 -2860.0
## - EXPERIMENTER 2 0.59304 9.7202 -2823.7
## [1] "Myeloid.DC.(CD11c+.CD123-) panel2 CBCS"
## [1] "DC.NK.(CD20-.CD14-) panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Warning: NAs introduced by coercion
## Start: AIC=169216
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 6.7723e+12 169216
## - MACHINE 1 3.0164e+09 6.7753e+12 169218
## - DATE 1 4.2524e+09 6.7766e+12 169219
## - EXPERIMENTER 4 2.6115e+10 6.7984e+12 169240
## [1] "DC.NK.(CD20-.CD14-) panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Start: AIC=-39238.49
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 0.000019 36.713 -39240
## - MACHINE 1 0.001576 36.715 -39240
## - EXPERIMENTER 4 0.037469 36.751 -39239
## <none> 36.713 -39238
##
## Step: AIC=-39240.49
## TARGET ~ MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - MACHINE 1 0.001592 36.715 -39242
## <none> 36.713 -39240
## - EXPERIMENTER 4 0.044057 36.757 -39240
## + DATE 1 0.000019 36.713 -39238
##
## Step: AIC=-39242.17
## TARGET ~ EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 36.715 -39242
## - EXPERIMENTER 4 0.042477 36.757 -39242
## + MACHINE 1 0.001592 36.713 -39240
## + DATE 1 0.000035 36.715 -39240
## Start: AIC=-3637.3
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 2 0.004490 2.8543 -3640.3
## <none> 2.8498 -3637.3
## - DATE 1 0.038747 2.8885 -3630.3
##
## Step: AIC=-3640.25
## TARGET ~ DATE
##
## Df Sum of Sq RSS AIC
## <none> 2.8543 -3640.3
## + EXPERIMENTER 2 0.004490 2.8498 -3637.3
## - DATE 1 0.056739 2.9110 -3629.1
## Start: AIC=-3592.18
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 2 0.012448 3.0614 -3593.5
## <none> 3.0490 -3592.2
## - DATE 1 0.049806 3.0988 -3583.4
##
## Step: AIC=-3593.46
## TARGET ~ DATE
##
## Df Sum of Sq RSS AIC
## <none> 3.0614 -3593.5
## + EXPERIMENTER 2 0.012448 3.0490 -3592.2
## - DATE 1 0.076323 3.1377 -3579.0
## [1] "DC.NK.(CD20-.CD14-) panel2 CBCS"
## [1] "MONOCYTES.(CD14+) panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Start: AIC=164231.2
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 3.1261e+08 3.6910e+12 164230
## <none> 3.6907e+12 164231
## - MACHINE 1 6.4379e+09 3.6972e+12 164244
## - EXPERIMENTER 4 7.8211e+10 3.7689e+12 164396
##
## Step: AIC=164229.9
## TARGET ~ MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 3.6910e+12 164230
## + DATE 1 3.1261e+08 3.6907e+12 164231
## - MACHINE 1 6.1375e+09 3.6972e+12 164242
## - EXPERIMENTER 4 9.3507e+10 3.7845e+12 164428
## [1] "MONOCYTES.(CD14+) panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Start: AIC=-41303.41
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 27.772 -41303
## - DATE 1 0.00961 27.781 -41303
## - MACHINE 1 0.04484 27.817 -41293
## - EXPERIMENTER 4 0.64815 28.420 -41141
## Start: AIC=-3701.44
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 2.5889 -3701.4
## - DATE 1 0.0081573 2.5971 -3701.3
## - EXPERIMENTER 2 0.0183342 2.6072 -3700.7
## Start: AIC=-3663.69
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 0.0006408 2.7401 -3665.5
## <none> 2.7394 -3663.7
## - EXPERIMENTER 2 0.0222645 2.7617 -3662.3
##
## Step: AIC=-3665.53
## TARGET ~ EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 2.7401 -3665.5
## + DATE 1 0.0006408 2.7394 -3663.7
## - EXPERIMENTER 2 0.0292265 2.7693 -3662.4
## [1] "MONOCYTES.(CD14+) panel2 CBCS"
## [1] "NK.(CD16+) panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Start: AIC=165905.6
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 4.5219e+12 165906
## - DATE 1 5.8761e+09 4.5278e+12 165914
## - MACHINE 1 5.8849e+09 4.5278e+12 165914
## - EXPERIMENTER 4 1.5000e+10 4.5369e+12 165925
## [1] "NK.(CD16+) panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Start: AIC=-42516.72
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 4 0.0108709 23.582 -42521
## <none> 23.571 -42517
## - MACHINE 1 0.0090782 23.580 -42516
## - DATE 1 0.0162401 23.587 -42514
##
## Step: AIC=-42521.31
## TARGET ~ DATE + MACHINE
##
## Df Sum of Sq RSS AIC
## - MACHINE 1 0.0061575 23.588 -42521
## <none> 23.582 -42521
## - DATE 1 0.0205788 23.602 -42517
## + EXPERIMENTER 4 0.0108709 23.571 -42517
##
## Step: AIC=-42521.38
## TARGET ~ DATE
##
## Df Sum of Sq RSS AIC
## <none> 23.588 -42521
## + MACHINE 1 0.0061575 23.582 -42521
## - DATE 1 0.0161827 23.604 -42518
## + EXPERIMENTER 4 0.0079501 23.580 -42516
## Start: AIC=-3874.8
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 2 0.0042268 2.0014 -3877.4
## <none> 1.9971 -3874.8
## - DATE 1 0.0115406 2.0087 -3872.9
##
## Step: AIC=-3877.39
## TARGET ~ DATE
##
## Df Sum of Sq RSS AIC
## <none> 2.0014 -3877.4
## - DATE 1 0.0082264 2.0096 -3876.6
## + EXPERIMENTER 2 0.0042268 1.9971 -3874.8
## Start: AIC=-3837
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 2 0.0055994 2.1190 -3839.2
## <none> 2.1134 -3837.0
## - DATE 1 0.0227898 2.1362 -3831.8
##
## Step: AIC=-3839.24
## TARGET ~ DATE
##
## Df Sum of Sq RSS AIC
## <none> 2.1190 -3839.2
## + EXPERIMENTER 2 0.0055994 2.1134 -3837.0
## - DATE 1 0.0178873 2.1369 -3835.6
## [1] "NK.(CD16+) panel2 CBCS"
## [1] "DC.NK.MONOCYTES.(CD3-.CD19-) panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Warning: NAs introduced by coercion
## Start: AIC=176929.5
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 2.1269e+09 1.7266e+13 176928
## <none> 1.7264e+13 176929
## - MACHINE 1 1.6919e+10 1.7281e+13 176936
## - EXPERIMENTER 4 2.0153e+11 1.7465e+13 177017
##
## Step: AIC=176928.5
## TARGET ~ MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 1.7266e+13 176928
## + DATE 1 2.1269e+09 1.7264e+13 176929
## - MACHINE 1 1.4947e+10 1.7281e+13 176934
## - EXPERIMENTER 4 2.3268e+11 1.7499e+13 177031
## [1] "DC.NK.MONOCYTES.(CD3-.CD19-) panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Start: AIC=-31606.78
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 103.00 -31607
## - DATE 1 0.17095 103.17 -31596
## - MACHINE 1 0.19657 103.20 -31595
## - EXPERIMENTER 4 1.34927 104.35 -31518
## Start: AIC=-2951.32
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 7.9579 -2951.3
## - EXPERIMENTER 2 0.099096 8.0570 -2947.1
## - DATE 1 0.133510 8.0915 -2942.2
## Start: AIC=-3038.57
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 6.9835 -3038.6
## - EXPERIMENTER 2 0.094612 7.0781 -3033.6
## - DATE 1 0.098365 7.0819 -3031.2
## [1] "DC.NK.MONOCYTES.(CD3-.CD19-) panel2 CBCS"
## [1] "NK.CD56HI panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Start: AIC=99320.83
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - MACHINE 1 50801 1404897053 99319
## <none> 1404846253 99321
## - EXPERIMENTER 4 1712436 1406558688 99323
## - DATE 1 920792 1405767044 99324
##
## Step: AIC=99319.13
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 1404897053 99319
## + MACHINE 1 50801 1404846253 99321
## - EXPERIMENTER 4 1819882 1406716935 99322
## - DATE 1 870744 1405767798 99322
## [1] "NK.CD56HI panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Start: AIC=-61711.29
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 4 0.00155069 1.7551 -61713
## - MACHINE 1 0.00014225 1.7537 -61713
## <none> 1.7536 -61711
## - DATE 1 0.00066448 1.7543 -61710
##
## Step: AIC=-61712.75
## TARGET ~ DATE + MACHINE
##
## Df Sum of Sq RSS AIC
## - MACHINE 1 0.00021573 1.7554 -61714
## <none> 1.7551 -61713
## + EXPERIMENTER 4 0.00155069 1.7536 -61711
## - DATE 1 0.00096796 1.7561 -61711
##
## Step: AIC=-61713.84
## TARGET ~ DATE
##
## Df Sum of Sq RSS AIC
## <none> 1.7554 -61714
## + MACHINE 1 0.00021573 1.7551 -61713
## + EXPERIMENTER 4 0.00162417 1.7537 -61713
## - DATE 1 0.00079685 1.7562 -61712
## Start: AIC=-5895.05
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 2 0.00007177 0.097114 -5898.6
## <none> 0.097042 -5895.0
## - DATE 1 0.00033553 0.097377 -5894.7
##
## Step: AIC=-5898.56
## TARGET ~ DATE
##
## Df Sum of Sq RSS AIC
## <none> 0.097114 -5898.6
## - DATE 1 0.00039627 0.097510 -5897.8
## + EXPERIMENTER 2 0.00007177 0.097042 -5895.0
## Start: AIC=-4836.98
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 2 0.0009967 0.47399 -4839.6
## - DATE 1 0.0012679 0.47426 -4837.2
## <none> 0.47299 -4837.0
##
## Step: AIC=-4839.58
## TARGET ~ DATE
##
## Df Sum of Sq RSS AIC
## <none> 0.47399 -4839.6
## - DATE 1 0.0031900 0.47718 -4837.1
## + EXPERIMENTER 2 0.0009967 0.47299 -4837.0
## [1] "NK.CD56HI panel2 CBCS"
## [1] "NK.CD56LO panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Start: AIC=165340.8
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 4.2225e+12 165341
## - MACHINE 1 4.6014e+09 4.2271e+12 165348
## - DATE 1 5.3515e+09 4.2278e+12 165349
## - EXPERIMENTER 4 1.4484e+10 4.2369e+12 165361
## [1] "NK.CD56LO panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO.x' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Start: AIC=-40323.54
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 31.622 -40324
## - DATE 1 0.020156 31.642 -40321
## - MACHINE 1 0.040634 31.663 -40316
## - EXPERIMENTER 4 0.108113 31.730 -40306
## Start: AIC=-3946.05
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 0.0002528 1.7953 -3948.0
## <none> 1.7951 -3946.1
## - EXPERIMENTER 2 0.0232470 1.8183 -3941.5
##
## Step: AIC=-3947.96
## TARGET ~ EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 1.7953 -3948.0
## + DATE 1 0.0002528 1.7951 -3946.1
## - EXPERIMENTER 2 0.0287863 1.8241 -3941.3
## Start: AIC=-3378.96
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 2 0.0060799 4.2015 -3382.0
## - DATE 1 0.0048066 4.2002 -3380.2
## <none> 4.1954 -3379.0
##
## Step: AIC=-3382
## TARGET ~ DATE
##
## Df Sum of Sq RSS AIC
## - DATE 1 0.0045288 4.2060 -3383.3
## <none> 4.2015 -3382.0
## + EXPERIMENTER 2 0.0060799 4.1954 -3379.0
##
## Step: AIC=-3383.28
## TARGET ~ 1
##
## Df Sum of Sq RSS AIC
## <none> 4.2060 -3383.3
## + DATE 1 0.0045288 4.2015 -3382.0
## + EXPERIMENTER 2 0.0058020 4.2002 -3380.2
## [1] "NK.CD56LO panel2 CBCS"
## [1] "Plasmacytoid.DC.(CD11c-.CD123+) panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Warning: NAs introduced by coercion
## Start: AIC=114200.2
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 806134 8581241410 114199
## - MACHINE 1 1942949 8582378226 114200
## <none> 8580435277 114200
## - EXPERIMENTER 4 45113760 8625549036 114235
##
## Step: AIC=114199
## TARGET ~ MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - MACHINE 1 1440278 8582681688 114198
## <none> 8581241410 114199
## + DATE 1 806134 8580435277 114200
## - EXPERIMENTER 4 55823747 8637065157 114244
##
## Step: AIC=114198.4
## TARGET ~ EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 8582681688 114198
## + MACHINE 1 1440278 8581241410 114199
## + DATE 1 303463 8582378226 114200
## - EXPERIMENTER 4 55149798 8637831487 114243
## [1] "Plasmacytoid.DC.(CD11c-.CD123+) panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Start: AIC=-34999.05
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 0.01281 65.029 -35000
## <none> 65.017 -34999
## - MACHINE 1 0.04135 65.058 -34996
## - EXPERIMENTER 4 0.39025 65.407 -34963
##
## Step: AIC=-34999.6
## TARGET ~ MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 65.029 -35000
## + DATE 1 0.01281 65.017 -34999
## - MACHINE 1 0.05762 65.087 -34995
## - EXPERIMENTER 4 0.56576 65.595 -34944
## Start: AIC=-2995.27
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - EXPERIMENTER 2 0.040401 7.4915 -2995.7
## <none> 7.4511 -2995.3
## - DATE 1 0.064654 7.5158 -2991.5
##
## Step: AIC=-2995.66
## TARGET ~ DATE
##
## Df Sum of Sq RSS AIC
## <none> 7.4915 -2995.7
## + EXPERIMENTER 2 0.040401 7.4511 -2995.3
## - DATE 1 0.035044 7.5266 -2994.6
## Start: AIC=-3363.11
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 0.000025 4.2961 -3365.1
## <none> 4.2961 -3363.1
## - EXPERIMENTER 2 0.070896 4.3670 -3356.2
##
## Step: AIC=-3365.11
## TARGET ~ EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 4.2961 -3365.1
## + DATE 1 0.000025 4.2961 -3363.1
## - EXPERIMENTER 2 0.081837 4.3780 -3356.5
## [1] "Plasmacytoid.DC.(CD11c-.CD123+) panel2 CBCS"
## [1] "Classical.monocytes.(CD16-.CD14+) panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Warning: NAs introduced by coercion
## Start: AIC=163499.4
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 1.4414e+08 3.3851e+12 163498
## <none> 3.3849e+12 163499
## - MACHINE 1 7.0322e+09 3.3920e+12 163514
## - EXPERIMENTER 4 7.1608e+10 3.4565e+12 163664
##
## Step: AIC=163497.7
## TARGET ~ MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 3.3851e+12 163498
## + DATE 1 1.4414e+08 3.3849e+12 163499
## - MACHINE 1 6.9956e+09 3.3921e+12 163513
## - EXPERIMENTER 4 8.7215e+10 3.4723e+12 163699
## [1] "Classical.monocytes.(CD16-.CD14+) panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Start: AIC=-48152.19
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - MACHINE 1 0.000037 10.993 -48154
## <none> 10.993 -48152
## - DATE 1 0.030247 11.023 -48134
## - EXPERIMENTER 4 0.082048 11.075 -48105
##
## Step: AIC=-48154.16
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 10.993 -48154
## + MACHINE 1 0.000037 10.993 -48152
## - DATE 1 0.031763 11.025 -48135
## - EXPERIMENTER 4 0.083194 11.076 -48106
## Start: AIC=-3831.43
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 0.0025004 2.1336 -3832.6
## - EXPERIMENTER 2 0.0124045 2.1435 -3831.6
## <none> 2.1311 -3831.4
##
## Step: AIC=-3832.65
## TARGET ~ EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 2.1336 -3832.6
## - EXPERIMENTER 2 0.0128645 2.1465 -3832.6
## + DATE 1 0.0025004 2.1311 -3831.4
## Start: AIC=-3599.38
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 0.00045 3.0167 -3601.3
## <none> 3.0162 -3599.4
## - EXPERIMENTER 2 0.18102 3.1973 -3564.5
##
## Step: AIC=-3601.28
## TARGET ~ EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 3.0167 -3601.3
## + DATE 1 0.00045 3.0162 -3599.4
## - EXPERIMENTER 2 0.20011 3.2168 -3562.4
## [1] "Classical.monocytes.(CD16-.CD14+) panel2 CBCS"
## [1] "DC.(HLA-DR+) panel2 COUNTS"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Warning in cor.test.default(as.numeric(merge[, c(ocCol)]),
## as.numeric(merge[, : Cannot compute exact p-value with ties
## Warning: NAs introduced by coercion
## Start: AIC=139868.1
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - DATE 1 7002698 1.9254e+11 139866
## - MACHINE 1 41044796 1.9257e+11 139868
## <none> 1.9253e+11 139868
## - EXPERIMENTER 4 4661827679 1.9719e+11 140057
##
## Step: AIC=139866.4
## TARGET ~ MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## - MACHINE 1 35041908 1.9257e+11 139866
## <none> 1.9254e+11 139866
## + DATE 1 7002698 1.9253e+11 139868
## - EXPERIMENTER 4 5817878274 1.9836e+11 140104
##
## Step: AIC=139865.9
## TARGET ~ EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 1.9257e+11 139866
## + MACHINE 1 35041908 1.9254e+11 139866
## + DATE 1 999810 1.9257e+11 139868
## - EXPERIMENTER 4 5786676280 1.9836e+11 140102
## [1] "DC.(HLA-DR+) panel2 FREQ"
## Warning in merge.data.frame(oc, manual, by.x = mergeOCCol, by.y =
## mergeManCol): column name 'NK.CD56LO' is duplicated in the result
##
## 0 1 3
## 668 129 5
## Start: AIC=-58883.52
## TARGET ~ DATE + MACHINE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 2.5797 -58884
## - MACHINE 1 0.001398 2.5811 -58882
## - DATE 1 0.001763 2.5815 -58880
## - EXPERIMENTER 4 0.039704 2.6194 -58779
## Start: AIC=-5650.04
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 0.14004 -5650.0
## - DATE 1 0.0019389 0.14198 -5642.9
## - EXPERIMENTER 2 0.0096720 0.14971 -5609.4
## Start: AIC=-6016.78
## TARGET ~ DATE + EXPERIMENTER
##
## Df Sum of Sq RSS AIC
## <none> 0.080876 -6016.8
## - DATE 1 0.0013851 0.082261 -6007.4
## - EXPERIMENTER 2 0.0085874 0.089463 -5953.4
## [1] "DC.(HLA-DR+) panel2 CBCS"
# results=results[-order(results$METRIC),]
results$COMP_LOOK =gsub(".", " ",results$COMP_LOOK,fixed = TRUE)
write.table(
results,
sep = "\t",
quote = FALSE,
file = paste0(dir,"testResults.txt"),
row.names = FALSE
)